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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
author iuc
date Mon, 02 Oct 2023 13:23:27 +0000
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1 <tool id="baredsc_2d" name="baredSC 2d" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
2 <description>Compute distribution for a pair of genes</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="edam_topics"/>
7 <edam_operations>
8 <edam_operation>operation_2495</edam_operation>
9 <edam_operation>operation_3463</edam_operation>
10 </edam_operations>
11 <xrefs>
12 <xref type="bio.tools">baredsc</xref>
13 </xrefs>
14 <expand macro="requirements"/>
15 <command detect_errors="exit_code"><![CDATA[
16 baredSC_2d
17 ## Required inputs:
18 @REQUIRED_INPUTS_2D@
19
20 ## Filter cells
21 @FILTER_CELLS@
22 ## MCMC
23 @MCMC_2D@
24 @BAREDSC_COMMON@
25 ## Plots
26 @PLOTS@
27 @PRETTYBINS_SPLITY_COLORSCALE_2D@
28 ## Advanced
29 @ADVANCED_COMMON_X@
30 @ADVANCED_COMMON_COMPLEMENT_2D@
31 @ADVANCED_BAREDSC_COMMON@
32 ## Outputs
33 --output output
34 --figure baredSC.$plots.image_file_format
35 --logevidence logevidence.txt &&
36 mkdir QC &&
37 mv baredSC_convergence.* QC &&
38 mv baredSC_p.$plots.image_file_format QC &&
39 mv baredSC_corner.* QC &&
40 mkdir output &&
41 mv baredSC_neff.txt output &&
42 @ORDER_OUTPUTS_2D@
43 ]]></command>
44 <inputs>
45 <expand macro="macro_input_counts"/>
46 <expand macro="macro_two_genes"/>
47 <expand macro="macro_filter_cells"/>
48 <section name="MCMC" title="MCMC parameters">
49 <expand macro="macro_MCMC_params_common_axis" axis="x" />
50 <expand macro="macro_MCMC_params_common_axis" axis="y" />
51 <expand macro="macro_scale_seed"/>
52 <expand macro="macro_MCMC_common_baredSC"/>
53 </section>
54 <section name="plots" title="Customize plots">
55 <expand macro="macro_plots"/>
56 <expand macro="macro_prettybins_axis" axis="x"/>
57 <expand macro="macro_prettybins_axis" axis="y"/>
58 <expand macro="macro_colorscale"/>
59 <expand macro="macro_splity"/>
60 </section>
61 <section name="advanced" title="Advanced parameters" expanded="false">
62 <expand macro="macro_advanced_common_axis" axis="x" default_osamppdf="4"/>
63 <expand macro="macro_advanced_common_axis" axis="y" default_osamppdf="4"/>
64 <expand macro="macro_advanced_evidence"/>
65 <expand macro="macro_advanced_common_baredSC"/>
66 <expand macro="macro_scaleprior"/>
67 </section>
68 </inputs>
69 <outputs>
70 <data format="npz" name="output" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: Numpy archive" from_work_dir="output.npz"/>
71 <data format="txt" name="neff" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: Neff" from_work_dir="output/baredSC_neff.txt"/>
72 <collection type="list" name="qc_plots" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: QC plots">
73 <discover_datasets pattern="baredSC_(?P&lt;identifier_0&gt;\S+)\.(?P&lt;ext&gt;.*)" directory="QC"/>
74 </collection>
75 <data format="tabular" name="pdf2d" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: mean PDF in matrix format" from_work_dir="output/baredSC_pdf2d.txt"/>
76 <data format="tabular" name="pdf2d_flat" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: PDF with error bar, one bin per line" from_work_dir="output/baredSC_pdf2d_flat.txt">
77 <actions>
78 <action name="column_names" type="metadata" default="x,y,low,mean,high,median" />
79 </actions>
80 </data>
81 <data format="png" name="plot" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: plot" from_work_dir="baredSC">
82 <change_format>
83 <when input="plots.image_file_format" value="png" format="png" />
84 <when input="plots.image_file_format" value="svg" format="svg" />
85 <when input="plots.image_file_format" value="pdf" format="pdf" />
86 </change_format>
87 </data>
88 <collection type="list" name="other_outputs" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: plots and txt">
89 <discover_datasets pattern="baredSC_(?P&lt;identifier_0&gt;\S+)\.(?P&lt;ext&gt;.*)"/>
90 </collection>
91 <data format="txt" name="logevidence" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: Log evidence" from_work_dir="logevidence.txt"/>
92 </outputs>
93 <tests>
94 <!-- First test I decreased the number of samples and bins to make it quicker-->
95 <test>
96 <conditional name="input_counts">
97 <param name="filetype" value="tabular"/>
98 <param name="input" value="nih3t3_generated_2d_2.txt"/>
99 </conditional>
100 <param name="geneXColName" value="0.5_0_0_0.5_x"/>
101 <param name="geneYColName" value="0.5_0_0_0.5_y"/>
102 <section name="MCMC">
103 <param name="nnorm" value="2"/>
104 <param name="nx" value="10"/>
105 <param name="ny" value="12"/>
106 <conditional name="automaticRestart">
107 <param name="set_minNeff" value="no"/>
108 </conditional>
109 <param name="nsampMCMC" value="20000"/>
110 </section>
111 <section name="plots">
112 <param name="prettyBinsx" value="50"/>
113 <param name="prettyBinsy" value="50"/>
114 </section>
115 <output name="output">
116 <assert_contents>
117 <has_size value="524174" delta="50000"/>
118 </assert_contents>
119 </output>
120 <output name="neff">
121 <assert_contents>
122 <has_text_matching expression="^1[0-2][0-9]\."/>
123 </assert_contents>
124 </output>
125 <output_collection name="qc_plots" count="3" type="list">
126 <element name="convergence" ftype="png">
127 <assert_contents>
128 <has_size value="35116" delta="3000"/>
129 </assert_contents>
130 </element>
131 <element name="p" ftype="png">
132 <assert_contents>
133 <has_size value="279538" delta="20000"/>
134 </assert_contents>
135 </element>
136 <element name="corner" ftype="png">
137 <assert_contents>
138 <has_size value="1450978" delta="100000"/>
139 </assert_contents>
140 </element>
141 </output_collection>
142 <output name="pdf2d" ftype="tabular">
143 <assert_contents>
144 <has_n_lines n="51"/>
145 <has_line_matching expression="xy\t0\.025\t0\.07500000000000001\t0\.125\t0\.17500000000000002\t0\.225\t0\.275\t0\.32500000000000007\t0\.375\t0\.42500000000000004\t0\.475\t0\.525\t0\.5750000000000001\t0\.625\t0\.675\t0\.7250000000000001\t0\.775\t0\.8250000000000001\t0\.875\t0\.925\t0\.9750000000000001\t1\.025\t1\.0750000000000002\t1\.125\t1\.1750000000000003\t1\.225\t1\.275\t1\.3250000000000002\t1\.375\t1\.4250000000000003\t1\.475\t1\.525\t1\.5750000000000002\t1\.625\t1\.6750000000000003\t1\.725\t1\.775\t1\.8250000000000002\t1\.875\t1\.9250000000000003\t1\.975\t2\.0250000000000004\t2\.075\t2\.125\t2\.175\t2\.225\t2\.2750000000000004\t2\.325\t2\.375\t2\.4250000000000003\t2\.475"/>
146 <has_text_matching expression="2\.5[0-9]+e-02\s+3\.[0-9]+e-02\s+[56]\.[0-9]+e-02"/>
147 </assert_contents>
148 </output>
149 <output name="pdf2d_flat" ftype="tabular">
150 <assert_contents>
151 <has_text_matching expression="x\s+y\s+low\s+mean\s+high\s+median"/>
152 <has_n_lines n="2501"/>
153 <has_line_matching expression="0\.025\s+0\.025[0-9]+\s+0\.002[0-9]+\s+0\.03[0-9]+\s+0\.0[67][0-9]+\s+0\.0[12][0-9]+"/>
154 </assert_contents>
155 </output>
156 <output name="plot" ftype="png">
157 <assert_contents>
158 <has_size value="40843" delta="4000"/>
159 </assert_contents>
160 </output>
161 <output_collection name="other_outputs" count="4" type="list">
162 <element name="p" ftype="txt">
163 <assert_contents>
164 <has_line_matching expression="name\s+low\s+median\s+high"/>
165 <has_line_matching expression="xy_mux[01]\s+0\.3[0-9]+\s+0\.3[0-9]+\s+0\.3[0-9]+"/>
166 <has_text_matching expression="xy_mux[01]\s+0\.9[0-9]+\s+1\.0[0-9]+\s+1\.0[0-9]+" />
167 <has_n_lines n="12"/>
168 </assert_contents>
169 </element>
170 <element name="corr" ftype="txt">
171 <assert_contents>
172 <has_n_lines n="2"/>
173 <has_line_matching expression="mean\tmedian\tlow\thigh\tpval\terror"/>
174 <has_text_matching expression="0\.9[0-9]+\s+0\.9[0-9]+\s+0\.8[0-9]+\s+0\.9[0-9]+\s+0\.00[7-9][0-9]+\s+0\.00[7-9][0-9]+\s+"/>
175 </assert_contents>
176 </element>
177 <element name="individuals" ftype="png">
178 <assert_contents>
179 <has_size value="56538" delta="5000"/>
180 </assert_contents>
181 </element>
182 <element name="median" ftype="png">
183 <assert_contents>
184 <has_size value="40829" delta="4000"/>
185 </assert_contents>
186 </element>
187 </output_collection>
188 <output name="logevidence">
189 <assert_contents>
190 <has_text_matching expression="^-81[0-9][0-9]\."/>
191 </assert_contents>
192 </output>
193 </test>
194 <!-- Second test pdf filtering cells title log scale-->
195 <test>
196 <conditional name="input_counts">
197 <param name="filetype" value="tabular"/>
198 <param name="input" value="nih3t3_generated_2d_2.txt"/>
199 </conditional>
200 <param name="geneXColName" value="0.5_0_0_0.5_x"/>
201 <param name="geneYColName" value="0.5_0_0_0.5_y"/>
202 <conditional name="filter">
203 <param name="nb" value="1"/>
204 <param name="metadata1ColName" value="0_0.5_0.5_0_group"/>
205 <param name="metadata1Values" value="1.0"/>
206 </conditional>
207 <section name="MCMC">
208 <param name="xmin" value="-12"/>
209 <param name="xmax" value="-7"/>
210 <param name="nx" value="25"/>
211 <param name="ymin" value="-12"/>
212 <param name="ymax" value="-7"/>
213 <param name="ny" value="25"/>
214 <param name="nnorm" value="2"/>
215 <param name="nsampMCMC" value="10000"/>
216 <conditional name="automaticRestart">
217 <param name="set_minNeff" value="yes"/>
218 <param name="minNeff" value="200"/>
219 </conditional>
220 <conditional name="scale">
221 <param name="type" value="log"/>
222 </conditional>
223 </section>
224 <section name="plots">
225 <param name="title" value="TEST2"/>
226 <param name="image_file_format" value="pdf"/>
227 <param name="splity" value="-10.5 -9.5"/>
228 </section>
229 <output name="output">
230 <assert_contents>
231 <has_size value="2690419" delta="200000"/>
232 </assert_contents>
233 </output>
234 <output name="neff">
235 <assert_contents>
236 <has_text_matching expression="^(10|9)[0-9][0-9]\."/>
237 </assert_contents>
238 </output>
239 <output_collection name="qc_plots" count="3" type="list">
240 <element name="convergence" ftype="pdf">
241 <assert_contents>
242 <has_size value="28184" delta="2000"/>
243 </assert_contents>
244 </element>
245 <element name="p" ftype="pdf">
246 <assert_contents>
247 <has_size value="800065" delta="80000"/>
248 </assert_contents>
249 </element>
250 <element name="corner" ftype="pdf">
251 <assert_contents>
252 <has_size value="1431497" delta="200000"/>
253 </assert_contents>
254 </element>
255 </output_collection>
256 <output name="pdf2d" ftype="tabular">
257 <assert_contents>
258 <has_n_lines n="26"/>
259 <has_line_matching expression="xy\s+-11\.9\s+-11\.7\s+-11\.5\s+-11\.3\s+-11\.1\s+-10\.9\s+-10\.7\s+-10\.5\s+-10\.3\s+-10\.1\s+-9\.9\s+-9\.7\s+-9\.5\s+-9\.3\s+-9\.1\s+-8\.9\s+-8\.7\s+-8\.5\s+-8\.3\s+-8\.1\s+-7\.9\s+-7\.699999999999999\s+-7\.5\s+-7\.299999999999999\s+-7\.1"/>
260 <has_text_matching expression="-1\.19[0-9]+e\+01\s+"/>
261 </assert_contents>
262 </output>
263 <output name="pdf2d_flat" ftype="tabular">
264 <assert_contents>
265 <has_text_matching expression="x\s+y\s+low\s+mean\s+high\s+median"/>
266 <has_n_lines n="626"/>
267 </assert_contents>
268 </output>
269 <output name="plot" ftype="pdf">
270 <assert_contents>
271 <has_size value="15541" delta="1000"/>
272 </assert_contents>
273 </output>
274 <output_collection name="other_outputs" count="10" type="list">
275 <element name="p" ftype="txt">
276 <assert_contents>
277 <has_line_matching expression="name\s+low\s+median\s+high"/>
278 <has_line_matching expression="xy_mux[01]\s+-8\.6[0-9]+\s+-8\.6[0-9]+\s+-8\.5[0-9]+"/>
279 <has_text_matching expression="xy_mux[01]\s+-10\.2[0-9]+\s+-10\.1[0-9]+\s+-10\.0[0-9]+" />
280 <has_n_lines n="12"/>
281 </assert_contents>
282 </element>
283 <element name="corr" ftype="txt">
284 <assert_contents>
285 <has_n_lines n="2"/>
286 <has_line_matching expression="mean\tmedian\tlow\thigh\tpval\terror"/>
287 <has_text_matching expression="0\.9[0-9]+\s+0\.9[0-9]+\s+0\.8[0-9]+\s+0\.9[0-9]+\s+0\.00[10|9][0-9]+\s+0\.00[10|9][0-9]+\s+"/>
288 </assert_contents>
289 </element>
290 <element name="individuals" ftype="pdf">
291 <assert_contents>
292 <has_size value="38594" delta="3000"/>
293 </assert_contents>
294 </element>
295 <element name="median" ftype="pdf">
296 <assert_contents>
297 <has_size value="15482" delta="1000"/>
298 </assert_contents>
299 </element>
300 <element name="split-10.5" ftype="pdf">
301 <assert_contents>
302 <has_size value="11801" delta="1000"/>
303 </assert_contents>
304 </element>
305 <element name="split-10.5_renorm" ftype="pdf">
306 <assert_contents>
307 <has_size value="13138" delta="1000"/>
308 </assert_contents>
309 </element>
310 <element name="split-10.5_pdf">
311 <assert_contents>
312 <has_text_matching expression="x\s+low1\s+mean1\s+high1\s+low2\s+mean2\s+high2"/>
313 <has_n_lines n="26"/>
314 <has_text_matching expression="-1\.19[0-9]+e\+01"/>
315 </assert_contents>
316 </element>
317 <element name="split-9.5" ftype="pdf">
318 <assert_contents>
319 <has_size value="11919" delta="1000"/>
320 </assert_contents>
321 </element>
322 <element name="split-9.5_renorm" ftype="pdf">
323 <assert_contents>
324 <has_size value="13145" delta="1000"/>
325 </assert_contents>
326 </element>
327 <element name="split-9.5_pdf">
328 <assert_contents>
329 <has_text_matching expression="x\s+low1\s+mean1\s+high1\s+low2\s+mean2\s+high2"/>
330 <has_n_lines n="26"/>
331 <has_text_matching expression="-1\.19[0-9]+e\+01\s+"/>
332 </assert_contents>
333 </element>
334 </output_collection>
335 <output name="logevidence">
336 <assert_contents>
337 <has_text_matching expression="^-40[0-9][0-9]\."/>
338 </assert_contents>
339 </output>
340 </test>
341 </tests>
342 <expand macro="helpcitations"/>
343 </tool>